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Veglia AJ, Bistolas KSI, Voolstra CR, Hume BCC, Ruscheweyh HJ, Planes S, Allemand D, Boissin E, Wincker P, Poulain J, Moulin C, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Galand PE, Gilson E, Lombard F, Pesant S, Reynaud S, Sunagawa S, Thomas OP, Troublé R, Zoccola D, Correa AMS, Vega Thurber RL. Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes. Commun Biol 2023; 6:566. [PMID: 37264063 DOI: 10.1038/s42003-023-04917-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 04/24/2023] [Indexed: 06/03/2023] Open
Abstract
Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.
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Affiliation(s)
- Alex J Veglia
- BioSciences Department, Rice University, Houston, TX, USA
| | | | | | | | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, Vladimir-Prelog-Weg 4, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Denis Allemand
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Clémentine Moulin
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75012, Paris, France
| | | | - Guillaume Iwankow
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Sarah Romac
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Michel Flores
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, 76100, Rehovot, Israel
| | - Didier Forcioli
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, LIA ROPSE, Monaco, France
| | - Paola Furla
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, LIA ROPSE, Monaco, France
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66650, Banyuls sur mer, France
| | - Eric Gilson
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Department of Medical Genetics, CHU of Nice, Nice, France
| | - Fabien Lombard
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, F-06230, Villefranche-sur-Mer, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, Vladimir-Prelog-Weg 4, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, University Road H91 TK33, Galway, Ireland
| | - Romain Troublé
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75012, Paris, France
| | - Didier Zoccola
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
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2
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Kambol R, Gatseva A, Gifford RJ. An endogenous lentivirus in the germline of a rodent. Retrovirology 2022; 19:30. [PMID: 36539757 PMCID: PMC9768972 DOI: 10.1186/s12977-022-00615-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
Lentiviruses (genus Lentivirus) are complex retroviruses that infect a broad range of mammals, including humans. Unlike many other retrovirus genera, lentiviruses have only rarely been incorporated into the mammalian germline. However, a small number of endogenous retrovirus (ERV) lineages have been identified, and these rare genomic "fossils" can provide crucial insights into the long-term history of lentivirus evolution. Here, we describe a previously unreported endogenous lentivirus lineage in the genome of the South African springhare (Pedetes capensis), demonstrating that the host range of lentiviruses has historically extended to rodents (order Rodentia). Furthermore, through comparative and phylogenetic analysis of lentivirus and ERV genomes, considering the biogeographic and ecological characteristics of host species, we reveal broader insights into the long-term evolutionary history of the genus.
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Affiliation(s)
- Roziah Kambol
- grid.412259.90000 0001 2161 1343School of Biological Sciences, Faculty of Applied Sciences, University Teknologi MARA, 40450 Shah Alam, Selangor Malaysia
| | - Anna Gatseva
- grid.301713.70000 0004 0393 3981MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, G61 1QH Glasgow UK
| | - Robert J. Gifford
- grid.301713.70000 0004 0393 3981MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, G61 1QH Glasgow UK
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3
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TLR7 and TLR8 evolution in lagomorphs: different patterns in the different lineages. Immunogenetics 2022; 74:475-485. [PMID: 35419618 DOI: 10.1007/s00251-022-01262-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/30/2022] [Indexed: 11/05/2022]
Abstract
Toll-like receptors (TLRs) are one of the most ancient and widely studied innate immune receptors responsible for host defense against invading pathogens. Among the known TLRs, TLR7 and TLR8 sense and recognize single-stranded (ss) RNAs with a dynamic evolutionary history. While TLR8 was lost in birds and duplicated in turtles and crocodiles, TLR7 is duplicated in some birds, but in other tetrapods, there is only one copy. In mammals, with the exception of lagomorphs, TLR7 and TLR8 are highly conserved. Here, we aim to study the evolution of TLR7 and TLR8 in mammals, with a special focus in the order Lagomorpha. By searching public sequence databases, conducting evolutionary analysis, and evaluating gene expression, we were able to confirm that TLR8 is absent in hares but widely expressed in the European rabbit. In contrast, TLR7 is absent in the European rabbit and quite divergent in hares. Our results suggest that, in lagomorphs, more in particular in leporids, TLR7 and TLR8 genes have evolved faster than in any other mammalian group. The long history of interaction with viruses and their location in highly dynamic telomeric regions might explain the pattern observed.
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4
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Zheng J, Wei Y, Han GZ. The diversity and evolution of retroviruses: perspectives from viral “fossils”. Virol Sin 2022; 37:11-18. [PMID: 35234634 PMCID: PMC8922424 DOI: 10.1016/j.virs.2022.01.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/12/2021] [Indexed: 01/19/2023] Open
Abstract
Retroviruses exclusively infect vertebrates, causing a variety of diseases. The replication of retroviruses requires reverse transcription and integration into host genomes. When infecting germline cells, retroviruses become inherited vertically, forming endogenous retroviruses (ERVs). ERVs document past viral infections, providing molecular fossils for studying the evolutionary history of retroviruses. In this review, we summarize the recent advances in understanding the diversity and evolution of retroviruses from the perspectives of viral fossils, and discuss the effects of ERVs on the evolution of host biology. Recent advances in understanding the diversity and evolution of retroviruses. Methods to analyze ERVs. The effects of ERVs on the evolution of host biology.
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Affiliation(s)
- Jialu Zheng
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Yutong Wei
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Guan-Zhu Han
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
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5
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Russell RM, Bibollet-Ruche F, Liu W, Sherrill-Mix S, Li Y, Connell J, Loy DE, Trimboli S, Smith AG, Avitto AN, Gondim MVP, Plenderleith LJ, Wetzel KS, Collman RG, Ayouba A, Esteban A, Peeters M, Kohler WJ, Miller RA, François-Souquiere S, Switzer WM, Hirsch VM, Marx PA, Piel AK, Stewart FA, Georgiev AV, Sommer V, Bertolani P, Hart JA, Hart TB, Shaw GM, Sharp PM, Hahn BH. CD4 receptor diversity represents an ancient protection mechanism against primate lentiviruses. Proc Natl Acad Sci U S A 2021; 118:e2025914118. [PMID: 33771926 PMCID: PMC8020793 DOI: 10.1073/pnas.2025914118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Infection with human and simian immunodeficiency viruses (HIV/SIV) requires binding of the viral envelope glycoprotein (Env) to the host protein CD4 on the surface of immune cells. Although invariant in humans, the Env binding domain of the chimpanzee CD4 is highly polymorphic, with nine coding variants circulating in wild populations. Here, we show that within-species CD4 diversity is not unique to chimpanzees but found in many African primate species. Characterizing the outermost (D1) domain of the CD4 protein in over 500 monkeys and apes, we found polymorphic residues in 24 of 29 primate species, with as many as 11 different coding variants identified within a single species. D1 domain amino acid replacements affected SIV Env-mediated cell entry in a single-round infection assay, restricting infection in a strain- and allele-specific fashion. Several identical CD4 polymorphisms, including the addition of N-linked glycosylation sites, were found in primate species from different genera, providing striking examples of parallel evolution. Moreover, seven different guenons (Cercopithecus spp.) shared multiple distinct D1 domain variants, pointing to long-term trans-specific polymorphism. These data indicate that the HIV/SIV Env binding region of the primate CD4 protein is highly variable, both within and between species, and suggest that this diversity has been maintained by balancing selection for millions of years, at least in part to confer protection against primate lentiviruses. Although long-term SIV-infected species have evolved specific mechanisms to avoid disease progression, primate lentiviruses are intrinsically pathogenic and have left their mark on the host genome.
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Affiliation(s)
- Ronnie M Russell
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | | | - Weimin Liu
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Scott Sherrill-Mix
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Yingying Li
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Jesse Connell
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Dorothy E Loy
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Stephanie Trimboli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Andrew G Smith
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Alexa N Avitto
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Marcos V P Gondim
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Lindsey J Plenderleith
- Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL Edinburgh, United Kingdom
- Centre for Immunity, Infection, and Evolution, University of Edinburgh, EH9 3FL Edinburgh, United Kingdom
| | - Katherine S Wetzel
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Ronald G Collman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Ahidjo Ayouba
- Recherche Translationnelle Appliquée au VIH et aux Maladies Infectieuses, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34090 Montpellier, France
| | - Amandine Esteban
- Recherche Translationnelle Appliquée au VIH et aux Maladies Infectieuses, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34090 Montpellier, France
| | - Martine Peeters
- Recherche Translationnelle Appliquée au VIH et aux Maladies Infectieuses, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34090 Montpellier, France
| | - William J Kohler
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
| | - Richard A Miller
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
| | | | - William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329
| | - Vanessa M Hirsch
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
| | - Preston A Marx
- Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70118
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA 70433
| | - Alex K Piel
- Department of Anthropology, University College London, WC1H 0BW London, United Kingdom
| | - Fiona A Stewart
- Department of Anthropology, University College London, WC1H 0BW London, United Kingdom
- School of Biological and Environmental Sciences, Liverpool John Moores University, L3 3AF Liverpool, United Kingdom
| | - Alexander V Georgiev
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Volker Sommer
- Department of Anthropology, University College London, WC1H 0BW London, United Kingdom
| | - Paco Bertolani
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, CB2 1QH Cambridge, United Kingdom
| | - John A Hart
- Lukuru Wildlife Research Foundation, Tshuapa-Lomami-Lualaba Project, BP 2012, Kinshasa, Democratic Republic of the Congo
| | - Terese B Hart
- Lukuru Wildlife Research Foundation, Tshuapa-Lomami-Lualaba Project, BP 2012, Kinshasa, Democratic Republic of the Congo
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Paul M Sharp
- Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL Edinburgh, United Kingdom
- Centre for Immunity, Infection, and Evolution, University of Edinburgh, EH9 3FL Edinburgh, United Kingdom
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104;
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
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6
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Mahé D, Matusali G, Deleage C, Alvarenga RLLS, Satie AP, Pagliuzza A, Mathieu R, Lavoué S, Jégou B, de França LR, Chomont N, Houzet L, Rolland AD, Dejucq-Rainsford N. Potential for Virus Endogenization in Humans through Testicular Germ Cell Infection: the Case of HIV. J Virol 2020; 94:e01145-20. [PMID: 32999017 PMCID: PMC7925188 DOI: 10.1128/jvi.01145-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/17/2020] [Indexed: 12/11/2022] Open
Abstract
Viruses have colonized the germ line of our ancestors on several occasions during evolution, leading to the integration in the human genome of viral sequences from over 30 retroviral groups and a few nonretroviruses. Among the recently emerged viruses infecting humans, several target the testis (e.g., human immunodeficiency virus [HIV], Zika virus, and Ebola virus). Here, we aimed to investigate whether human testicular germ cells (TGCs) can support integration by HIV, a contemporary retrovirus that started to spread in the human population during the last century. We report that albeit alternative receptors enabled HIV-1 binding to TGCs, HIV virions failed to infect TGCs in vitro Nevertheless, exposure of TGCs to infected lymphocytes, naturally present in the testis from HIV+ men, led to HIV-1 entry, integration, and early protein expression. Similarly, cell-associated infection or bypassing viral entry led to HIV-1 integration in a spermatogonial cell line. Using DNAscope, HIV-1 and simian immunodeficiency virus (SIV) DNA were detected within a few TGCs in the testis from one infected patient, one rhesus macaque, and one African green monkey in vivo Molecular landscape analysis revealed that early TGCs were enriched in HIV early cofactors up to integration and had overall low antiviral defenses compared with testicular macrophages and Sertoli cells. In conclusion, our study reveals that TGCs can support the entry and integration of HIV upon cell-associated infection. This could represent a way for this contemporary virus to integrate into our germ line and become endogenous in the future, as happened during human evolution for a number of viruses.IMPORTANCE Viruses have colonized the host germ line on many occasions during evolution to eventually become endogenous. Here, we aimed at investigating whether human testicular germ cells (TGCs) can support such viral invasion by studying HIV interactions with TGCs in vitro Our results indicate that isolated primary TGCs express alternative HIV-1 receptors, allowing virion binding but not entry. However, HIV-1 entered and integrated into TGCs upon cell-associated infection and produced low levels of viral proteins. In vivo, HIV-1 and SIV DNA was detected in a few TGCs. Molecular landscape analysis showed that TGCs have overall weak antiviral defenses. Altogether, our results indicate that human TGCs can support HIV-1 early replication, including integration, suggesting potential for endogenization in future generations.
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Affiliation(s)
- Dominique Mahé
- Université Rennes, INSERM, EHESP, IRSET (Institut de Recherche en Santé, Environnement et Travail)-UMR_S1085, Rennes, France
| | - Giulia Matusali
- Université Rennes, INSERM, EHESP, IRSET (Institut de Recherche en Santé, Environnement et Travail)-UMR_S1085, Rennes, France
| | - Claire Deleage
- Université Rennes, INSERM, EHESP, IRSET (Institut de Recherche en Santé, Environnement et Travail)-UMR_S1085, Rennes, France
| | - Raquel L L S Alvarenga
- Laboratory of Cellular Biology, Department of Morphology, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Anne-Pascale Satie
- Université Rennes, INSERM, EHESP, IRSET (Institut de Recherche en Santé, Environnement et Travail)-UMR_S1085, Rennes, France
| | - Amélie Pagliuzza
- Department of Microbiology, Infectiology and Immunology, Faculty of Medecine, Université de Montréal, and Centre de Recherche du CHUM, Montréal, Quebec, Canada
| | - Romain Mathieu
- Centre Hospitalier Universitaire de Pontchaillou, Service Urologie, Rennes, France
| | - Sylvain Lavoué
- Centre Hospitalier Universitaire de Pontchaillou, Centre de Coordination des Prélèvements, Rennes, France
| | - Bernard Jégou
- Université Rennes, INSERM, EHESP, IRSET (Institut de Recherche en Santé, Environnement et Travail)-UMR_S1085, Rennes, France
| | - Luiz R de França
- Laboratory of Cellular Biology, Department of Morphology, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Nicolas Chomont
- Department of Microbiology, Infectiology and Immunology, Faculty of Medecine, Université de Montréal, and Centre de Recherche du CHUM, Montréal, Quebec, Canada
| | - Laurent Houzet
- Université Rennes, INSERM, EHESP, IRSET (Institut de Recherche en Santé, Environnement et Travail)-UMR_S1085, Rennes, France
| | - Antoine D Rolland
- Université Rennes, INSERM, EHESP, IRSET (Institut de Recherche en Santé, Environnement et Travail)-UMR_S1085, Rennes, France
| | - Nathalie Dejucq-Rainsford
- Université Rennes, INSERM, EHESP, IRSET (Institut de Recherche en Santé, Environnement et Travail)-UMR_S1085, Rennes, France
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7
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van der Kuyl AC, Berkhout B. Viruses in the reproductive tract: On their way to the germ line? Virus Res 2020; 286:198101. [PMID: 32710926 DOI: 10.1016/j.virusres.2020.198101] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/17/2020] [Accepted: 07/18/2020] [Indexed: 01/13/2023]
Abstract
Studies of vertebrate genomes have indicated that all species contain in their chromosomes stretches of DNA with sequence similarity to viral genomes. How such 'endogenous' viral elements (EVEs) ended up in host genomes is usually explained in general terms such as 'they entered the germ line at some point during evolution'. This seems a correct statement, but is also rather imprecise. The vast number of endogenous viral sequences suggest that common routes to the 'germ line' may exist, as relying on chance alone may not easily explain the abundance of EVEs in modern mammalian genomes. An increasing number of virus types have been detected in human semen and a growing number of studies have reported on viral infections that cause male infertility or subfertility and on viral infections that threaten in vitro fertilisation practices. Thus, it is timely to survey the pathway(s) that viruses can use to gain access to the human germ line. Embryo transfer and semen quality studies in livestock form another source of relevant information because virus infection during reproduction is clearly unwanted, as is the case for the human situation. In this review, studies on viruses in the male and female reproductive tract and in the early embryo will be discussed to propose a plausible viral route to the mammalian germ line.
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Affiliation(s)
- Antoinette Cornelia van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers, Amsterdam, The Netherlands.
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers, Amsterdam, The Netherlands
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8
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Le Tortorec A, Matusali G, Mahé D, Aubry F, Mazaud-Guittot S, Houzet L, Dejucq-Rainsford N. From Ancient to Emerging Infections: The Odyssey of Viruses in the Male Genital Tract. Physiol Rev 2020; 100:1349-1414. [PMID: 32031468 DOI: 10.1152/physrev.00021.2019] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The male genital tract (MGT) is the target of a number of viral infections that can have deleterious consequences at the individual, offspring, and population levels. These consequences include infertility, cancers of male organs, transmission to the embryo/fetal development abnormalities, and sexual dissemination of major viral pathogens such as human immunodeficiency virus (HIV) and hepatitis B virus. Lately, two emerging viruses, Zika and Ebola, have additionally revealed that the human MGT can constitute a reservoir for viruses cleared from peripheral circulation by the immune system, leading to their sexual transmission by cured men. This represents a concern for future epidemics and further underlines the need for a better understanding of the interplay between viruses and the MGT. We review here how viruses, from ancient viruses that integrated the germline during evolution through old viruses (e.g., papillomaviruses originating from Neanderthals) and more modern sexually transmitted infections (e.g., simian zoonotic HIV) to emerging viruses (e.g., Ebola and Zika) take advantage of genital tract colonization for horizontal dissemination, viral persistence, vertical transmission, and endogenization. The MGT immune responses to viruses and the impact of these infections are discussed. We summarize the latest data regarding the sources of viruses in semen and the complex role of this body fluid in sexual transmission. Finally, we introduce key animal findings that are relevant for our understanding of viral infection and persistence in the human MGT and suggest future research directions.
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Affiliation(s)
- Anna Le Tortorec
- University of Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S1085, Rennes, France
| | - Giulia Matusali
- University of Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S1085, Rennes, France
| | - Dominique Mahé
- University of Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S1085, Rennes, France
| | - Florence Aubry
- University of Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S1085, Rennes, France
| | - Séverine Mazaud-Guittot
- University of Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S1085, Rennes, France
| | - Laurent Houzet
- University of Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S1085, Rennes, France
| | - Nathalie Dejucq-Rainsford
- University of Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S1085, Rennes, France
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9
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Abstract
Recent discoveries of contemporary genotypes of hepatitis B virus and parvovirus B19 in ancient human remains demonstrate that little genetic change has occurred in these viruses over 4,500-6,000 years. Endogenous viral elements in host genomes provide separate evidence that viruses similar to many major contemporary groups circulated 100 million years ago or earlier. In this Opinion article, we argue that the extraordinary conservation of virus genome sequences is best explained by a niche-filling model in which fitness optimization is rapidly achieved in their specific hosts. Whereas short-term substitution rates reflect the accumulation of tolerated sequence changes within adapted genomes, longer-term rates increasingly resemble those of their hosts as the evolving niche moulds and effectively imprisons the virus in co-adapted virus-host relationships. Contrastingly, viruses that jump hosts undergo strong and stringent adaptive selection as they maximize their fit to their new niche. This adaptive capability may paradoxically create evolutionary stasis in long-term host relationships. While viruses can evolve and adapt rapidly, their hosts may ultimately shape their longer-term evolution.
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10
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Águeda-Pinto A, Lemos de Matos A, Pinheiro A, Neves F, de Sousa-Pereira P, Esteves PJ. Not so unique to Primates: The independent adaptive evolution of TRIM5 in Lagomorpha lineage. PLoS One 2019; 14:e0226202. [PMID: 31830084 PMCID: PMC6907815 DOI: 10.1371/journal.pone.0226202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 11/21/2019] [Indexed: 02/07/2023] Open
Abstract
The plethora of restriction factors with the ability to inhibit the replication of retroviruses have been widely studied and genetic hallmarks of evolutionary selective pressures in Primates have been well documented. One example is the tripartite motif-containing protein 5 alpha (TRIM5α), a cytoplasmic factor that restricts retroviral infection in a species-specific fashion. In Lagomorphs, similarly to what has been observed in Primates, the specificity of TRIM5 restriction has been assigned to the PRYSPRY domain. In this study, we present the first insight of an intra-genus variability within the Lagomorpha TRIM5 PRYSPRY domain. Remarkably, and considering just the 32 residue-long v1 region of this domain, the deduced amino acid sequences of Daurian pika (Ochotona dauurica) and steppe pika (O. pusilla) evidenced a high divergence when compared to the remaining Ochotona species, presenting values of 44% and 66% of amino acid differences, respectively. The same evolutionary pattern was also observed when comparing the v1 region of two Sylvilagus species members (47% divergence). However, and unexpectedly, the PRYSPRY domain of Lepus species exhibited a great conservation. Our results show a high level of variation in the PRYSPRY domain of Lagomorpha species that belong to the same genus. This suggests that, throughout evolution, the Lagomorpha TRIM5 should have been influenced by constant selective pressures, likely as a result of multiple different retroviral infections.
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Affiliation(s)
- Ana Águeda-Pinto
- CIBIO/InBio—Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto,Porto, Portugal
| | - Ana Lemos de Matos
- Center for Immunotherapy, Vaccines, and Virotherapy (CIVV), The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Ana Pinheiro
- CIBIO/InBio—Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto,Porto, Portugal
| | - Fabiana Neves
- CIBIO/InBio—Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Patrícia de Sousa-Pereira
- CIBIO/InBio—Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto,Porto, Portugal
| | - Pedro J. Esteves
- CIBIO/InBio—Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto,Porto, Portugal
- CITS—Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU,Gandra, Portugal
- * E-mail:
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11
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Mage RG, Esteves PJ, Rader C. Rabbit models of human diseases for diagnostics and therapeutics development. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 92:99-104. [PMID: 30339876 PMCID: PMC6364550 DOI: 10.1016/j.dci.2018.10.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/07/2018] [Accepted: 10/11/2018] [Indexed: 05/03/2023]
Abstract
This review presents some examples of studies using the European rabbit (Oryctolagus cuniculus) that have led to, and continue to, contribute to advancement of understanding of human diseases as well as therapeutics development. In addition, we tabulate FDA-approved rabbit polyclonal and rabbit monoclonal antibodies (mAbs) that are used for diagnostic applications, as well as an overview of some "humanized" or otherwise altered rabbit mAbs that are in initial phase I, II, or advanced to phase III clinical trials. Information about endogenous retriviruses learned from studies of rabbits and other members of the order Lagomorpha are summarized as this knowledge now applies to new therapeutics being developed for several human diseases including Multiple Sclerosis, Type 1 Diabetes and Cancer.
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Affiliation(s)
- Rose G Mage
- Laboratory of Immune System Biology, NIAID, NIH, Bldg 10 11N311, 10 Center Drive, Bethesda, MD, 20892-1892, USA.
| | - Pedro J Esteves
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal; Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (CESPU), Gandra, Portugal
| | - Christoph Rader
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, 33458, USA
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12
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Whole-genome comparison of endogenous retrovirus segregation across wild and domestic host species populations. Proc Natl Acad Sci U S A 2018; 115:11012-11017. [PMID: 30297425 PMCID: PMC6205466 DOI: 10.1073/pnas.1815056115] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Although recent advances in sequencing and computational analyses have facilitated use of endogenous retroviruses (ERVs) for deciphering coevolution among retroviruses and their hosts, sampling effects from different host populations present major challenges. Here we utilize available whole-genome data from wild and domesticated European rabbit (Oryctolagus cuniculus sp.) populations, sequenced as DNA pools by paired-end Illumina technology, for identifying segregating reference as well as nonreference ERV loci, to reveal their variation along the host phylogeny and domestication history. To produce new viruses, retroviruses must insert a proviral DNA copy into the host nuclear DNA. Occasional proviral insertions into the host germline have been passed down through generations as inherited ERVs during millions of years. These ERVs represent retroviruses that were active at the time of infection and thus present a remarkable record of historical virus-host associations. To examine segregating ERVs in host populations, we apply a reference library search strategy for anchoring ERV-associated short-sequence read pairs from pooled whole-genome sequences to reference genome assembly positions. We show that most ERVs segregate along host phylogeny but also uncover radiation of some ERVs, identified as segregating loci among wild and domestic rabbits. The study targets pertinent issues regarding genome sampling when examining virus-host evolution from the genomic ERV record and offers improved scope regarding common strategies for single-nucleotide variant analyses in host population comparative genomics.
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13
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de Sousa-Pereira P, Abrantes J, Baldauf HM, Esteves PJ. Evolutionary studies on the betaretrovirus RERV-H in the Leporidae family reveal an endogenization in the ancestor of Oryctolagus, Bunolagus and Pentalagus at 9 million years ago. Virus Res 2017; 262:24-29. [PMID: 29208424 DOI: 10.1016/j.virusres.2017.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 12/01/2017] [Accepted: 12/01/2017] [Indexed: 01/31/2023]
Abstract
RERV-H was first identified in human tissues and mistaken for a human exogenous retrovirus. However, the integration sites carried by this virus showed that it was instead a European rabbit (Oryctolagus cuniculus) endogenous retrovirus. The first clones retrieved from European rabbit samples represented defective proviruses, although estimation of proviral copy numbers found in the European rabbit genome ranged from hundreds to thousands. Screening for the presence of RERV-H showed the absence of the virus in two other lagomorphs, pika (Ochotona) and hares (Lepus), which diverged from rabbits about 35 and 12 million years ago, respectively. Using a PCR-based approach, samples of seven different Lagomorph genera were tested for the presence of RERV-H. It was possible to amplify a proviral fragment corresponding to RNaseH from Oryctolagus, Bunolagus and Pentalagus genomic samples. The amplification of proviral DNA in species other than Oryctolagus revealed that this virus was endogenized in their common ancestor, roughly 9 million years ago. Using the European rabbit genome sequence OryCun2.0, it was possible to find multiple copies spread throughout the genome and several complete proviral genomes were retrieved. Some copies contained full open reading frames for all viral components. The lack of a complete genome in the other Lagomorph species did not allow further analyses of the provirus, although more deleterious mutations were found in Bunolagus and Pentalagus than in Oryctolagus RNaseH-amplified sequences. To what extent RERV-H and other endogenous viruses might have had an impact on the rabbit genome and its immune system remains elusive.
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Affiliation(s)
- Patricia de Sousa-Pereira
- InBIO - Research Network in Biodiversity and Evolutionary Biology, CIBIO, Campus de Vairão, Universidade do Porto, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal; Max von Pettenkofer-Institute for Virology, Ludwig-Maximilians-University Munich, Munich, Germany.
| | - Joana Abrantes
- InBIO - Research Network in Biodiversity and Evolutionary Biology, CIBIO, Campus de Vairão, Universidade do Porto, Vairão, Portugal.
| | - Hanna-Mari Baldauf
- Max von Pettenkofer-Institute for Virology, Ludwig-Maximilians-University Munich, Munich, Germany.
| | - Pedro José Esteves
- InBIO - Research Network in Biodiversity and Evolutionary Biology, CIBIO, Campus de Vairão, Universidade do Porto, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal; CITS - Centro de Investigação em Tecnologias de Saúde, CESPU, Gandra, Portugal.
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14
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Hayward A. Origin of the retroviruses: when, where, and how? Curr Opin Virol 2017; 25:23-27. [PMID: 28672160 PMCID: PMC5962544 DOI: 10.1016/j.coviro.2017.06.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 06/11/2017] [Accepted: 06/19/2017] [Indexed: 12/04/2022]
Abstract
Retroviruses are a virus family of considerable medical and veterinary importance. Until recently, very little was known about deep retroviral origins. New research supports a marine origin of retroviruses, ∼460–550 million years ago. The evolutionary events leading to the origin of retroviruses remain obscure. Improved understanding of Metaviridae diversity and evolution are required for this.
Retroviruses are a virus family of considerable medical and veterinary importance. Additionally, it is now clear that endogenous retroviruses (ERVs) comprise significant portions of vertebrate genomes. Until recently, very little was known about the deep evolutionary origins of retroviruses. However, advances in genomics and bioinformatics have opened the way for great strides in understanding. Recent research employing a wide variety of bioinformatic approaches has demonstrated that retroviruses evolved during the early Palaeozoic Era, between 460 and 550 million years ago, providing the oldest inferred date estimate for any virus group. This finding presents an important framework to investigate the evolutionary transitions that led to the emergence of the retroviruses, offering potential insights into the infectious origins of a major group of pathogenic viruses.
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Affiliation(s)
- Alexander Hayward
- Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Penryn, TR10 9FE, United Kingdom.
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15
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Fernandes JD, Faust TB, Strauli NB, Smith C, Crosby DC, Nakamura RL, Hernandez RD, Frankel AD. Functional Segregation of Overlapping Genes in HIV. Cell 2017; 167:1762-1773.e12. [PMID: 27984726 DOI: 10.1016/j.cell.2016.11.031] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 09/29/2016] [Accepted: 11/15/2016] [Indexed: 11/28/2022]
Abstract
Overlapping genes pose an evolutionary dilemma as one DNA sequence evolves under the selection pressures of multiple proteins. Here, we perform systematic statistical and mutational analyses of the overlapping HIV-1 genes tat and rev and engineer exhaustive libraries of non-overlapped viruses to perform deep mutational scanning of each gene independently. We find a "segregated" organization in which overlapped sites encode functional residues of one gene or the other, but never both. Furthermore, this organization eliminates unfit genotypes, providing a fitness advantage to the population. Our comprehensive analysis reveals the extraordinary manner in which HIV minimizes the constraint of overlapping genes and repurposes that constraint to its own advantage. Thus, overlaps are not just consequences of evolutionary constraints, but rather can provide population fitness advantages.
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Affiliation(s)
- Jason D Fernandes
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA; Program in Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Tyler B Faust
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA; Tetrad Program, Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Nicolas B Strauli
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA
| | - Cynthia Smith
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - David C Crosby
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Robert L Nakamura
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Alan D Frankel
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA.
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16
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Greenwood EJD, Matheson NJ, Wals K, van den Boomen DJH, Antrobus R, Williamson JC, Lehner PJ. Temporal proteomic analysis of HIV infection reveals remodelling of the host phosphoproteome by lentiviral Vif variants. eLife 2016; 5:e18296. [PMID: 27690223 PMCID: PMC5085607 DOI: 10.7554/elife.18296] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 09/28/2016] [Indexed: 12/20/2022] Open
Abstract
Viruses manipulate host factors to enhance their replication and evade cellular restriction. We used multiplex tandem mass tag (TMT)-based whole cell proteomics to perform a comprehensive time course analysis of >6500 viral and cellular proteins during HIV infection. To enable specific functional predictions, we categorized cellular proteins regulated by HIV according to their patterns of temporal expression. We focussed on proteins depleted with similar kinetics to APOBEC3C, and found the viral accessory protein Vif to be necessary and sufficient for CUL5-dependent proteasomal degradation of all members of the B56 family of regulatory subunits of the key cellular phosphatase PP2A (PPP2R5A-E). Quantitative phosphoproteomic analysis of HIV-infected cells confirmed Vif-dependent hyperphosphorylation of >200 cellular proteins, particularly substrates of the aurora kinases. The ability of Vif to target PPP2R5 subunits is found in primate and non-primate lentiviral lineages, and remodeling of the cellular phosphoproteome is therefore a second ancient and conserved Vif function.
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Affiliation(s)
- Edward JD Greenwood
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Nicholas J Matheson
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Kim Wals
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Dick JH van den Boomen
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Robin Antrobus
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - James C Williamson
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Paul J Lehner
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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17
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Hron T, Farkašová H, Padhi A, Pačes J, Elleder D. Life History of the Oldest Lentivirus: Characterization of ELVgv Integrations in the Dermopteran Genome. Mol Biol Evol 2016; 33:2659-69. [DOI: 10.1093/molbev/msw149] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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18
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Naville M, Volff JN. Endogenous Retroviruses in Fish Genomes: From Relics of Past Infections to Evolutionary Innovations? Front Microbiol 2016; 7:1197. [PMID: 27555838 PMCID: PMC4977317 DOI: 10.3389/fmicb.2016.01197] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 07/19/2016] [Indexed: 12/16/2022] Open
Abstract
The increasing availability of fish genome sequences has allowed to gain new insights into the diversity and host distribution of retroviruses in fish and other vertebrates. This distribution can be assessed through the identification and analysis of endogenous retroviruses, which are proviral remnants of past infections integrated in genomes. Retroviral sequences are probably important for evolution through their ability to induce rearrangements and to contribute regulatory and coding sequences; they may also protect their host against new infections. We argue that the current mass of genome sequences will soon strongly improve our understanding of retrovirus diversity and evolution in aquatic animals, with the identification of new/re-emerging elements and host resistance genes that restrict their infectivity.
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Affiliation(s)
- Magali Naville
- Génomique Évolutive des Poissons, Institut de Génomique Fonctionnelle de Lyon, École Normale Supérieure de Lyon, CNRS, Université Lyon 1 Lyon, France
| | - Jean-Nicolas Volff
- Génomique Évolutive des Poissons, Institut de Génomique Fonctionnelle de Lyon, École Normale Supérieure de Lyon, CNRS, Université Lyon 1 Lyon, France
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19
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Abstract
Among the most fundamental questions in viral evolutionary biology are how fast viruses evolve and how evolutionary rates differ among viruses and fluctuate through time. Traditionally, viruses are loosely classed into two groups: slow-evolving DNA viruses and fast-evolving RNA viruses. As viral evolutionary rate estimates become more available, it appears that the rates are negatively correlated with the measurement timescales and that the boundary between the rates of DNA and RNA viruses might not be as clear as previously thought. In this study, we collected 396 viral evolutionary rate estimates across almost all viral genome types and replication strategies, and we examined their rate dynamics. We showed that the time-dependent rate phenomenon exists across multiple levels of viral taxonomy, from the Baltimore classification viral groups to genera. We also showed that, by taking the rate decay dynamics into account, a clear division between the rates of DNA and RNA viruses as well as reverse-transcribing viruses could be recovered. Surprisingly, despite large differences in their biology, our analyses suggested that the rate decay speed is independent of viral types and thus might be useful for better estimation of the evolutionary time scale of any virus. To illustrate this, we used our model to reestimate the evolutionary timescales of extant lentiviruses, which were previously suggested to be very young by standard phylogenetic analyses. Our analyses suggested that these viruses are millions of years old, in agreement with paleovirological evidence, and therefore, for the first time, reconciled molecular analyses of ancient and extant viruses. IMPORTANCE This work provides direct evidence that viral evolutionary rate estimates decay with their measurement timescales and that the rate decay speeds do not differ significantly among viruses despite the vast differences in their molecular features. After adjustment for the rate decay dynamics, the division between the rates of double-stranded DNA (dsDNA), single-stranded RNA (ssRNA), and ssDNA/reverse-transcribing viruses could be seen more clearly than before. Our results provide a guideline for further improvement of the molecular clock. As a demonstration of this, we used our model to reestimate the timescales of modern lentiviruses, which were previously thought to be very young, and concluded that they are millions of years old. This result matches the estimate from paleovirological analyses, thus bridging the gap between ancient and extant viral evolutionary studies.
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20
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Adaptive Gene Loss? Tracing Back the Pseudogenization of the Rabbit CCL8 Chemokine. J Mol Evol 2016; 83:12-25. [PMID: 27306379 DOI: 10.1007/s00239-016-9747-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 05/03/2016] [Indexed: 10/21/2022]
Abstract
Studies of the process of pseudogenization have widened our understanding of adaptive evolutionary change. In Rabbit, an alteration at the second extra-cellular loop of the CCR5 chemokine receptor was found to be associated with the pseudogenization of one of its prime ligands, the chemokine CCL8. This relationship has raised questions about the existence of a causal link between both events, which would imply adaptive gene loss. This hypothesis is evaluated here by tracing back the history of the genetic modifications underlying the chemokine pseudogenization. The obtained data indicate that mutations at receptor and ligand genes occurred after the lineage split of New World Leporids versus Old World Leporids and prior to the generic split of the of Old World species studied, which occurred an estimated 8-9 million years ago. More important, they revealed the emergence, before this zoographical split, of a "slippery" nucleotide motif (CCCCGGG) at the 3' region of CCL8-exon2. Such motives are liable of generating +1G or -1G frameshifts, which could, however, be overcome by "translesion" synthesis or somatic reversion. The CCL8 pseudogenization in the Old World lineage was apparently initiated by three synapomorphic point mutations at the exon2-intron2 boundary which provide at short range premature terminating codons, independently of the reading frame imposed by the slippery motif. The presence of this motif in New World Leporids might allow verifying this scenario. The importance of CCL8-CCR5 signaling in parasite-host interaction would suggest that the CCL8 knock-out in Old World populations might be related to changes in pathogenic environment.
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21
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Evolutionary study of leporid CD4 reveals a hotspot of genetic variability within the D2 domain. Immunogenetics 2016; 68:477-482. [PMID: 26979977 DOI: 10.1007/s00251-016-0909-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 03/03/2016] [Indexed: 10/22/2022]
Abstract
CD4 is the major receptor on T helper cells involved in the uptake of human immunodeficiency virus (HIV) or simian immunodeficiency virus (SIV) into their host cells. Evolutionary studies of CD4 in primates revealed signatures of positive selection in the D1 domain that interacts with primate exogenous lentivirus gp120 proteins. Here, we studied the evolution of CD4 in lagomorphs by comparing sequences obtained for the genera Oryctolagus, Sylvilagus, Lepus, and Ochotona. Our results reveal an overall higher divergence in lagomorphs compared to primates with highest divergence in the D2 domain. A detailed analysis of a small fragment of 33 nucleotides coding for amino acids 169 to 179 in the D2 domain showed dramatic amino acid alterations with a dN/dS value of 3.2 for lagomorphs, suggesting that CD4 is under strong positive selection in this particular region. Within each leporid genus, no significant amino acid changes were observed for the D2 domain which indicates that the genetic differentiation occurred in the ancestor of each genus before the species radiation. The rabbit endogenous lentivirus type K (RELIK) found in leporids shares high structural similarity with HIV which suggests a possible interaction between RELIK and CD4. The presence of RELIK in the studied leporids, the high structural similarity to modern-day exogenous lentiviruses and the absence of exogenous lentiviruses in leporids, allows us to hypothesize that this endogenous retrovirus, that was most probably exogenous in the past, drove the divergent evolution of leporid CD4.
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22
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Meng F, Chen C, Wan H, Zhou Q. [Advances of lentiviral vectors]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2015; 17:870-6. [PMID: 25539614 PMCID: PMC6000409 DOI: 10.3779/j.issn.1009-3419.2014.12.09] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Lentiviral vectors are currently very effective tools in molecular and cell experiment. Lentiviral vector, a kind of retroviral vectors, has a number of unique advantages in target gene transferation, for example, the ability of transfection to the dividing or nondividing cells, its high efficiency of transfection and a capacity of large target gene fragments. This paper describes the sources of lentiviral vectors, molecular characteristics, research progress, etc.
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Affiliation(s)
- Fanrong Meng
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenviroment, Tianjin Lung Cancer Institute,
Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Chen Chen
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenviroment, Tianjin Lung Cancer Institute,
Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Haisu Wan
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenviroment, Tianjin Lung Cancer Institute,
Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Qinghua Zhou
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenviroment, Tianjin Lung Cancer Institute,
Tianjin Medical University General Hospital, Tianjin 300052, China
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23
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Pinheiro A, Neves F, Lemos de Matos A, Abrantes J, van der Loo W, Mage R, Esteves PJ. An overview of the lagomorph immune system and its genetic diversity. Immunogenetics 2015; 68:83-107. [PMID: 26399242 DOI: 10.1007/s00251-015-0868-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 08/31/2015] [Indexed: 01/11/2023]
Abstract
Our knowledge of the lagomorph immune system remains largely based upon studies of the European rabbit (Oryctolagus cuniculus), a major model for studies of immunology. Two important and devastating viral diseases, rabbit hemorrhagic disease and myxomatosis, are affecting European rabbit populations. In this context, we discuss the genetic diversity of the European rabbit immune system and extend to available information about other lagomorphs. Regarding innate immunity, we review the most recent advances in identifying interleukins, chemokines and chemokine receptors, Toll-like receptors, antiviral proteins (RIG-I and Trim5), and the genes encoding fucosyltransferases that are utilized by rabbit hemorrhagic disease virus as a portal for invading host respiratory and gut epithelial cells. Evolutionary studies showed that several genes of innate immunity are evolving by strong natural selection. Studies of the leporid CCR5 gene revealed a very dramatic change unique in mammals at the second extracellular loop of CCR5 resulting from a gene conversion event with the paralogous CCR2. For the adaptive immune system, we review genetic diversity at the loci encoding antibody variable and constant regions, the major histocompatibility complex (RLA) and T cells. Studies of IGHV and IGKC genes expressed in leporids are two of the few examples of trans-species polymorphism observed outside of the major histocompatibility complex. In addition, we review some endogenous viruses of lagomorph genomes, the importance of the European rabbit as a model for human disease studies, and the anticipated role of next-generation sequencing in extending knowledge of lagomorph immune systems and their evolution.
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Affiliation(s)
- Ana Pinheiro
- InBIO-Research Network in Biodiversity and Evolutionary Biology, CIBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr. 7, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal
- SaBio-IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain
| | - Fabiana Neves
- InBIO-Research Network in Biodiversity and Evolutionary Biology, CIBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr. 7, 4485-661, Vairão, Portugal
- UMIB/UP-Unidade Multidisciplinar de Investigação Biomédica, Universidade do Porto, Porto, Portugal
| | - Ana Lemos de Matos
- Department of Molecular Genetics & Microbiology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Joana Abrantes
- InBIO-Research Network in Biodiversity and Evolutionary Biology, CIBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr. 7, 4485-661, Vairão, Portugal
| | - Wessel van der Loo
- InBIO-Research Network in Biodiversity and Evolutionary Biology, CIBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr. 7, 4485-661, Vairão, Portugal
| | - Rose Mage
- NIAID, NIH, Bethesda, MD, 20892, USA
| | - Pedro José Esteves
- InBIO-Research Network in Biodiversity and Evolutionary Biology, CIBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr. 7, 4485-661, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal.
- CITS-Centro de Investigação em Tecnologias de Saúde, CESPU, Gandra, Portugal.
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Abstract
Endogenous retroviruses comprise millions of discrete genetic loci distributed within the genomes of extant vertebrates. These sequences, which are clearly related to exogenous retroviruses, represent retroviral infections of the deep past, and their abundance suggests that retroviruses were a near-constant presence throughout the evolutionary history of modern vertebrates. Endogenous retroviruses contribute in myriad ways to the evolution of host genomes, as mutagens and as sources of genetic novelty (both coding and regulatory) to be acted upon by the twin engines of random genetic drift and natural selection. Importantly, the richness and complexity of endogenous retrovirus data can be used to understand how viruses spread and adapt on evolutionary timescales by combining population genetics and evolutionary theory with a detailed understanding of retrovirus biology (gleaned from the study of extant retroviruses). In addition to revealing the impact of viruses on organismal evolution, such studies can help us better understand, by looking back in time, how life-history traits, as well as ecological and geological events, influence the movement of viruses within and between populations.
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Affiliation(s)
- Welkin E Johnson
- Biology Department, Boston College, Chestnut Hill, Massachusetts 02467;
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McCarthy KR, Kirmaier A, Autissier P, Johnson WE. Evolutionary and Functional Analysis of Old World Primate TRIM5 Reveals the Ancient Emergence of Primate Lentiviruses and Convergent Evolution Targeting a Conserved Capsid Interface. PLoS Pathog 2015; 11:e1005085. [PMID: 26291613 PMCID: PMC4546234 DOI: 10.1371/journal.ppat.1005085] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 07/15/2015] [Indexed: 12/29/2022] Open
Abstract
The widespread distribution of lentiviruses among African primates, and the lack of severe pathogenesis in many of these natural reservoirs, are taken as evidence for long-term co-evolution between the simian immunodeficiency viruses (SIVs) and their primate hosts. Evidence for positive selection acting on antiviral restriction factors is consistent with virus-host interactions spanning millions of years of primate evolution. However, many restriction mechanisms are not virus-specific, and selection cannot be unambiguously attributed to any one type of virus. We hypothesized that the restriction factor TRIM5, because of its unique specificity for retrovirus capsids, should accumulate adaptive changes in a virus-specific fashion, and therefore, that phylogenetic reconstruction of TRIM5 evolution in African primates should reveal selection by lentiviruses closely related to modern SIVs. We analyzed complete TRIM5 coding sequences of 22 Old World primates and identified a tightly-spaced cluster of branch-specific adaptions appearing in the Cercopithecinae lineage after divergence from the Colobinae around 16 million years ago. Functional assays of both extant TRIM5 orthologs and reconstructed ancestral TRIM5 proteins revealed that this cluster of adaptations in TRIM5 specifically resulted in the ability to restrict Cercopithecine lentiviruses, but had no effect (positive or negative) on restriction of other retroviruses, including lentiviruses of non-Cercopithecine primates. The correlation between lineage-specific adaptations and ability to restrict viruses endemic to the same hosts supports the hypothesis that lentiviruses closely related to modern SIVs were present in Africa and infecting the ancestors of Cercopithecine primates as far back as 16 million years ago, and provides insight into the evolution of TRIM5 specificity. Old World primates in Africa are reservoir hosts for more than 40 species of simian immunodeficiency viruses (SIVs), including the sources of the human immunodeficiency viruses, HIV-1 and HIV-2. To investigate the prehistoric origins of these lentiviruses, we looked for patterns of evolution in the antiviral host gene TRIM5 that would reflect selection by lentiviruses during evolution of African primates. We identified a pattern of adaptive changes unique to the TRIM5 proteins of a subset of African monkeys that suggests that the ancestors of these viruses emerged between 11–16 million years ago, and by reconstructing and comparing the function of ancestral TRIM5 proteins with extant TRIM5 proteins, we confirmed that these adaptations confer specificity for their modern descendants, the SIVs.
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Affiliation(s)
- Kevin R. McCarthy
- Harvard Program in Virology, Harvard Medical School, Boston, Massachusetts, United States of America
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Andrea Kirmaier
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Patrick Autissier
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Welkin E. Johnson
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
- * E-mail:
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26
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Lemos de Matos A, de Sousa-Pereira P, Lissovsky AA, van der Loo W, Melo-Ferreira J, Cui J, Esteves PJ. Endogenization of mouse mammary tumor virus (MMTV)-like elements in genomes of pikas (Ochotona sp.). Virus Res 2015; 210:22-6. [PMID: 26151606 DOI: 10.1016/j.virusres.2015.06.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 06/24/2015] [Accepted: 06/25/2015] [Indexed: 11/29/2022]
Abstract
Despite the finding in European rabbit and other leporid genomes of the first ever described endogenous lentivirus and of a European rabbit exclusive endogenous gammaretrovirus, until now no exogenous retroviruses have been isolated in Lagomorpha species. Nevertheless, looking for the presence of endogenous retroviruses (ERVs) in the species genomes could lead to the discovery of retroviral lineages yet to be found in Lagomorpha. Different mammalian genomes harbor endogenous viral sequences phylogenetically close to the betaretrovirus mouse mammary tumor virus (MMTV), propelling us to look for such retroviral "fossil" in American pika (Ochotona princeps) and European rabbit (Oryctolagus cuniculus) genomes. By performing genomic mining using MMTV gag and LTR as query sequences, we found that such viral elements were absent from the European rabbit genome. Oppositely, significant matches were found in American pika, and more importantly, a nearly complete MMTV-like virus (Pika-BERV) was identified. Using Pika-BERV gag and LTR as templates, we found similar sequences endogenized in different pika (Ochotona sp.) species. The orthology of the LTR flanking region between some pika species supported shared ancestry of specific endogenous betaretroviruses, while in other pika species similar sequences, but not orthologous, should have resulted from independent insertions. Our study supports the possible existence of infecting exogenous betaretroviruses for a long term, after the divergence of Ochotonidae from Leporidae, but yet to be identified.
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Affiliation(s)
- Ana Lemos de Matos
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos/InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal.
| | - Patrícia de Sousa-Pereira
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos/InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Andrey A Lissovsky
- Zoological Museum, Moscow State Lomonosov University, 125009, B. Nikitskaya 6, Moscow, Russia
| | - Wessel van der Loo
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos/InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - José Melo-Ferreira
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos/InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal
| | - Jie Cui
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore 169857, Singapore
| | - Pedro J Esteves
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos/InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal; CITS - Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU, 4585-116 Gandra, Portugal.
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Tenth International Foamy Virus Conference 2014--achievements and perspectives. Viruses 2015; 7:1651-66. [PMID: 25835535 PMCID: PMC4411671 DOI: 10.3390/v7041651] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 03/19/2015] [Accepted: 03/23/2015] [Indexed: 01/10/2023] Open
Abstract
For the past two decades, scientists from around the world, working on different aspects of foamy virus (FV) research, have gathered in different research institutions almost every two years to present their recent results in formal talks, to discuss their ongoing studies informally, and to initiate fruitful collaborations. In this report we review the 2014 anniversary conference to share the meeting summary with the virology community and hope to arouse interest by other researchers to join this exciting field. The topics covered included epidemiology, virus molecular biology, and immunology of FV infection in non-human primates, cattle, and humans with zoonotic FV infections, as well as recent findings on endogenous FVs. Several topics focused on virus replication and interactions between viral and cellular proteins. Use of FV in biomedical research was highlighted with presentations on using FV vectors for gene therapy and FV proteins as scaffold for vaccine antigen presentation. On behalf of the FV community, this report also includes a short tribute to commemorate Prof. Axel Rethwilm, one of the leading experts in the field of retrovirology and foamy viruses, who passed away 29 July 2014.
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Aiewsakun P, Katzourakis A. Endogenous viruses: Connecting recent and ancient viral evolution. Virology 2015; 479-480:26-37. [PMID: 25771486 DOI: 10.1016/j.virol.2015.02.011] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 12/15/2014] [Accepted: 02/04/2015] [Indexed: 12/17/2022]
Abstract
The rapid rates of viral evolution allow us to reconstruct the recent history of viruses in great detail. This feature, however, also results in rapid erosion of evolutionary signal within viral molecular data, impeding studies of their deep history. Thus, the further back in time, the less accurate the inference becomes. Furthermore, reconstructing complex histories of transmission can be challenging, especially where extinct viral lineages are concerned. This problem has been partially solved by the discovery of viruses embedded in host genomes, known as endogenous viral elements (EVEs). Some of these endogenous viruses are derived from ancient relatives of extant viruses, allowing us to better examine ancient viral host range, geographical distribution and transmission routes. Moreover, our knowledge of viral evolutionary timescales and rate dynamics has also been greatly improved by their discovery, thereby bridging the gap between recent and ancient viral evolution.
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Affiliation(s)
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.
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29
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Han GZ, Worobey M. A primitive endogenous lentivirus in a colugo: insights into the early evolution of lentiviruses. Mol Biol Evol 2014; 32:211-5. [PMID: 25349288 DOI: 10.1093/molbev/msu297] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Lentiviruses infect a wide range of mammal species. Much remains unknown about their deep history and host distribution. Here, we report the discovery of an endogenous lentivirus within the genome of the Sunda flying lemur (Galeopterus variegatus) (which we designate "Galeopterus variegatus endogenous lentivirus" [GvaELV]). We estimate the GvaELV genome invasion to have occurred more than 14 Ma, supporting an ancient origin of the lentivirus clade and an ancient lentiviral infection in colugo. Phylogenetic analyses show that GvaELV is a sister group of all previously known lentiviruses. The GvaELV genome appears to possess some primitive genomic features of a lentivirus, encoding not only a trans-activator of transcription (tat) gene but also two additional putative accessory genes that share no discernible similarity with other lentiviral accessory genes. The discovery of GvaELV provides novel insights into the prehistory and host distribution of lentivirus.
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Affiliation(s)
- Guan-Zhu Han
- Department of Ecology and Evolutionary Biology, University of Arizona
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona
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30
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Hron T, Fábryová H, Pačes J, Elleder D. Endogenous lentivirus in Malayan colugo (Galeopterus variegatus), a close relative of primates. Retrovirology 2014; 11:84. [PMID: 25280529 PMCID: PMC4198772 DOI: 10.1186/s12977-014-0084-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/09/2014] [Indexed: 12/02/2022] Open
Abstract
Background A significant fraction of mammalian genomes is composed of endogenous retroviral (ERV) sequences that are formed by germline infiltration of various retroviruses. In contrast to other retroviral genera, lentiviruses only rarely form ERV copies. We performed a computational search aimed at identification of novel endogenous lentiviruses in vertebrate genomes. Findings Using the in silico strategy, we have screened 104 publicly available vertebrate genomes for the presence of endogenous lentivirus sequences. In addition to the previously described cases, the search revealed the presence of endogenous lentivirus in the genome of Malayan colugo (Galeopterus variegatus). At least three complete copies of this virus, denoted ELVgv, were detected in the colugo genome, and approximately one hundred solo LTR sequences. The assembled consensus sequence of ELVgv had typical lentivirus genome organization including three predicted accessory genes. Phylogenetic analysis placed this virus as a distinct subgroup within the lentivirus genus. The time of insertion into the dermopteran lineage was estimated to be more than thirteen million years ago. Conclusions We report the discovery of the first endogenous lentivirus in the mammalian order Dermoptera, which is a taxon close to the Primates. Lentiviruses have infiltrated the mammalian germline several times across millions of years. The colugo virus described here represents possibly the oldest documented endogenization event and its discovery can lead to new insights into lentivirus evolution. This is also the first report of an endogenous lentivirus in an Asian mammal, indicating a long-term presence of this retrovirus family in Asian continent. Electronic supplementary material The online version of this article (doi:10.1186/s12977-014-0084-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tomáš Hron
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220, Prague, Czech Republic.
| | - Helena Fábryová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220, Prague, Czech Republic.
| | - Jan Pačes
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220, Prague, Czech Republic.
| | - Daniel Elleder
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220, Prague, Czech Republic.
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31
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Kamath PL, Elleder D, Bao L, Cross PC, Powell JH, Poss M. The population history of endogenous retroviruses in mule deer (Odocoileus hemionus). J Hered 2013; 105:173-87. [PMID: 24336966 DOI: 10.1093/jhered/est088] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mobile elements are powerful agents of genomic evolution and can be exceptionally informative markers for investigating species and population-level evolutionary history. While several studies have utilized retrotransposon-based insertional polymorphisms to resolve phylogenies, few population studies exist outside of humans. Endogenous retroviruses are LTR-retrotransposons derived from retroviruses that have become stably integrated in the host genome during past infections and transmitted vertically to subsequent generations. They offer valuable insight into host-virus co-evolution and a unique perspective on host evolutionary history because they integrate into the genome at a discrete point in time. We examined the evolutionary history of a cervid endogenous gammaretrovirus (CrERVγ) in mule deer (Odocoileus hemionus). We sequenced 14 CrERV proviruses (CrERV-in1 to -in14), and examined the prevalence and distribution of 13 proviruses in 262 deer among 15 populations from Montana, Wyoming, and Utah. CrERV absence in white-tailed deer (O. virginianus), identical 5' and 3' long terminal repeat (LTR) sequences, insertional polymorphism, and CrERV divergence time estimates indicated that most endogenization events occurred within the last 200000 years. Population structure inferred from CrERVs (F ST = 0.008) and microsatellites (θ = 0.01) was low, but significant, with Utah, northwestern Montana, and a Helena herd being particularly differentiated. Clustering analyses indicated regional structuring, and non-contiguous clustering could often be explained by known translocations. Cluster ensemble results indicated spatial localization of viruses, specifically in deer from northeastern and western Montana. This study demonstrates the utility of endogenous retroviruses to elucidate and provide novel insight into both ERV evolutionary history and the history of contemporary host populations.
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Affiliation(s)
- Pauline L Kamath
- the US Geological Survey, Northern Rocky Mountain Science Center, Bozeman, MT 59715
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32
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Hayward A, Grabherr M, Jern P. Broad-scale phylogenomics provides insights into retrovirus-host evolution. Proc Natl Acad Sci U S A 2013; 110:20146-51. [PMID: 24277832 PMCID: PMC3864273 DOI: 10.1073/pnas.1315419110] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Genomic data provide an excellent resource to improve understanding of retrovirus evolution and the complex relationships among viruses and their hosts. In conjunction with broad-scale in silico screening of vertebrate genomes, this resource offers an opportunity to complement data on the evolution and frequency of past retroviral spread and so evaluate future risks and limitations for horizontal transmission between different host species. Here, we develop a methodology for extracting phylogenetic signal from large endogenous retrovirus (ERV) datasets by collapsing information to facilitate broad-scale phylogenomics across a wide sample of hosts. Starting with nearly 90,000 ERVs from 60 vertebrate host genomes, we construct phylogenetic hypotheses and draw inferences regarding the designation, host distribution, origin, and transmission of the Gammaretrovirus genus and associated class I ERVs. Our results uncover remarkable depths in retroviral sequence diversity, supported within a phylogenetic context. This finding suggests that current infectious exogenous retrovirus diversity may be underestimated, adding credence to the possibility that many additional exogenous retroviruses may remain to be discovered in vertebrate taxa. We demonstrate a history of frequent horizontal interorder transmissions from a rodent reservoir and suggest that rats may have acted as important overlooked facilitators of gammaretrovirus spread across diverse mammalian hosts. Together, these results demonstrate the promise of the methodology used here to analyze large ERV datasets and improve understanding of retroviral evolution and diversity for utilization in wider applications.
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Affiliation(s)
- Alexander Hayward
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala Biomedical Centre, SE-75123 Uppsala, Sweden
| | - Manfred Grabherr
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala Biomedical Centre, SE-75123 Uppsala, Sweden
| | - Patric Jern
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala Biomedical Centre, SE-75123 Uppsala, Sweden
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33
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Cook R, Leroux C, Issel C. Equine infectious anemia and equine infectious anemia virus in 2013: A review. Vet Microbiol 2013; 167:181-204. [DOI: 10.1016/j.vetmic.2013.09.031] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 09/16/2013] [Accepted: 09/21/2013] [Indexed: 10/26/2022]
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Yap MW, Stoye JP. Apparent effect of rabbit endogenous lentivirus type K acquisition on retrovirus restriction by lagomorph Trim5αs. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120498. [PMID: 23938750 PMCID: PMC3758185 DOI: 10.1098/rstb.2012.0498] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To test the hypothesis that rabbit endogenous lentivirus type K (RELIK) could play a role in shaping the evolution of TRIM5α, the susceptibility of viruses containing the RELIK capsid (CA) to TRIM5 restriction was evaluated. RELIK CA-containing viruses were susceptible to the TRIM5αs from Old World monkeys but were unaffected by most ape or New World monkey factors. TRIM5αs from various lagomorph species were also isolated and tested for anti-retroviral activity. The TRIM5αs from both cottontail rabbit and pika restrict a range of retroviruses, including HIV-1, HIV-2, FIV, EIAV and N-MLV. TRIM5αs from the European and cottontail rabbit, which have previously been found to contain RELIK, also restricted RELIK CA-containing viruses, whereas a weaker restriction was observed with chimeric TRIM5α containing the B30.2 domain from the pika, which lacks RELIK. Taken together, these results could suggest that the pika had not been exposed to exogenous RELIK and that endogenized RELIK might exert a selective pressure on lagomorph TRIM5α.
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Affiliation(s)
| | - Jonathan P. Stoye
- Division of Virology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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35
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Lee A, Nolan A, Watson J, Tristem M. Identification of an ancient endogenous retrovirus, predating the divergence of the placental mammals. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120503. [PMID: 23938752 PMCID: PMC3758187 DOI: 10.1098/rstb.2012.0503] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The evolutionary arms race between mammals and retroviruses has long been recognized as one of the oldest host-parasite interactions. Rapid evolution rates in exogenous retroviruses have often made accurate viral age estimations highly problematic. Endogenous retroviruses (ERVs), however, integrate into the germline of their hosts, and are subjected to their evolutionary rates. This study describes, for the first time, a retroviral orthologue predating the divergence of placental mammals, giving it a minimum age of 104-110 Myr. Simultaneously, other orthologous selfish genetic elements (SGEs), inserted into the ERV sequence, provide evidence for the oldest individual mammalian-wide interspersed repeat and medium-reiteration frequency interspersed repeat mammalian repeats, with the same minimum age. The combined use of shared SGEs and reconstruction of viral orthologies defines new limits and increases maximum 'lookback' times, with subsequent implications for the field of paleovirology.
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Affiliation(s)
- Adam Lee
- Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Alison Nolan
- Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, UK
| | - Jason Watson
- Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, UK
| | - Michael Tristem
- Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, UK
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36
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Abstract
The majority of retroviral envelope glycoproteins characterized to date are typical of type I viral fusion proteins, having a receptor binding subunit associated with a fusion subunit. The fusion subunits of lentiviruses and alpha-, beta-, delta- and gammaretroviruses have a very conserved domain organization and conserved features of secondary structure, making them suitable for phylogenetic analyses. Such analyses, along with sequence comparisons, reveal evidence of numerous recombination events in which retroviruses have acquired envelope glycoproteins from heterologous sequences. Thus, the envelope gene (env) can have a history separate from that of the polymerase gene (pol), which is the most commonly used gene in phylogenetic analyses of retroviruses. Focusing on the fusion subunits of the genera listed above, we describe three distinct types of retroviral envelope glycoproteins, which we refer to as gamma-type, avian gamma-type and beta-type. By tracing these types within the ‘fossil record’ provided by endogenous retroviruses, we show that they have surprisingly distinct evolutionary histories and dynamics, with important implications for cross-species transmissions and the generation of novel lineages. These findings validate the utility of env sequences in contributing phylogenetic signal that enlarges our understanding of retrovirus evolution.
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Affiliation(s)
- Jamie E Henzy
- Biology Department, Boston College, , Chestnut Hill, MA 02467, USA
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37
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Katzourakis A. Paleovirology: inferring viral evolution from host genome sequence data. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120493. [PMID: 23938747 DOI: 10.1098/rstb.2012.0493] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Aris Katzourakis
- Department of Zoology, University of Oxford, , Oxford OX1 3PS, UK
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McCarthy KR, Schmidt AG, Kirmaier A, Wyand AL, Newman RM, Johnson WE. Gain-of-sensitivity mutations in a Trim5-resistant primary isolate of pathogenic SIV identify two independent conserved determinants of Trim5α specificity. PLoS Pathog 2013; 9:e1003352. [PMID: 23675300 PMCID: PMC3649984 DOI: 10.1371/journal.ppat.1003352] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Accepted: 03/25/2013] [Indexed: 11/18/2022] Open
Abstract
Retroviral capsid recognition by Trim5 blocks productive infection. Rhesus macaques harbor three functionally distinct Trim5 alleles: Trim5αQ, Trim5αTFP and Trim5CypA. Despite the high degree of amino acid identity between Trim5αQ and Trim5αTFP alleles, the Q/TFP polymorphism results in the differential restriction of some primate lentiviruses, suggesting these alleles differ in how they engage these capsids. Simian immunodeficiency virus of rhesus macaques (SIVmac) evolved to resist all three alleles. Thus, SIVmac provides a unique opportunity to study a virus in the context of the Trim5 repertoire that drove its evolution in vivo. We exploited the evolved rhesus Trim5α resistance of this capsid to identify gain-of-sensitivity mutations that distinguish targets between the Trim5αQ and Trim5αTFP alleles. While both alleles recognize the capsid surface, Trim5αQ and Trim5αTFP alleles differed in their ability to restrict a panel of capsid chimeras and single amino acid substitutions. When mapped onto the structure of the SIVmac239 capsid N-terminal domain, single amino acid substitutions affecting both alleles mapped to the β-hairpin. Given that none of the substitutions affected Trim5αQ alone, and the fact that the β-hairpin is conserved among retroviral capsids, we propose that the β-hairpin is a molecular pattern widely exploited by Trim5α proteins. Mutations specifically affecting rhesus Trim5αTFP (without affecting Trim5αQ) surround a site of conservation unique to primate lentiviruses, overlapping the CPSF6 binding site. We believe targeting this site is an evolutionary innovation driven specifically by the emergence of primate lentiviruses in Africa during the last 12 million years. This modularity in targeting may be a general feature of Trim5 evolution, permitting different regions of the PRYSPRY domain to evolve independent interactions with capsid. TRIM5α is an intrinsic immunity protein that blocks retrovirus infection through a specific interaction with the viral capsid. Uniquely among primates, rhesus macaques harbor three functionally distinct kinds of Trim5 alleles: rhTrim5αTFP, rhTrim5αQ and rhTrim5CypA. SIVmac239, a simian immunodeficiency virus that causes AIDS in rhesus macaques, is resistant to all three, whereas its relative, the human AIDS virus HIV-1, is inhibited by rhTrim5αTFP and rhTrim5αQ alleles. We exploited this difference between these two retroviruses to figure out how Trim5α proteins recognize viral capsids. By combining mutagenesis, structural biology and evolutionary data we determined that both rhTrim5αTFP and rhTrim5αQ recognize a conserved structure common to all retroviral capsids. However, we also found evidence suggesting that rhTrim5αTFP evolved to recognize an additional target that is specifically conserved among primate immunodeficiency viruses. Molecular evolutionary analysis indicates that this expanded function appeared in a common ancestor of modern African monkeys sometime between 9–12 million years ago, and that it thereafter continued to be modified by strong evolutionary pressure. Our results provide insight into the evolutionary flexibility of Trim5α-capsid interactions, and support the notion that viruses related to modern HIV and SIV have been present in Africa for millions of years.
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Affiliation(s)
- Kevin R. McCarthy
- Harvard Program in Virology, Harvard Medical School, Boston, Massachusetts, United States of America
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Aaron G. Schmidt
- Laboratory of Molecular Medicine, Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Andrea Kirmaier
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Allison L. Wyand
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Ruchi M. Newman
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Welkin E. Johnson
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
- * E-mail:
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39
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Birth, decay, and reconstruction of an ancient TRIMCyp gene fusion in primate genomes. Proc Natl Acad Sci U S A 2013; 110:E583-92. [PMID: 23319649 DOI: 10.1073/pnas.1216542110] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
TRIM5 is a host antiviral gene with an evolutionary history of genetic conflict with retroviruses. The TRIMCyp gene encodes a protein fusion of TRIM5 effector domains with the capsid-binding ability of a retrotransposed CyclophilinA (CypA), resulting in novel antiviral specificity against lentiviruses. Previous studies have identified two independent primate TRIMCyp fusions that evolved within the past 6 My. Here, we describe an ancient primate TRIMCyp gene (that we call TRIMCypA3), which evolved in the common ancestor of simian primates 43 Mya. Gene reconstruction shows that CypA3 encoded an intact, likely active, TRIMCyp antiviral gene, which was subject to selective constraints for at least 10 My, followed by pseudogenization or loss in all extant primates. Despite its decayed status, we found TRIMCypA3 gene fusion transcripts in several primates. We found that the reconstructed "newly born" TrimCypA3 encoded robust and broad retroviral restriction activity but that this broad activity was lost via eight amino acid changes over the course of the next 10 My. We propose that TRIMCypA3 arose in response to a viral pathogen encountered by ancestral primates but was subsequently pseudogenized or lost due to a lack of selective pressure. Much like imprints of ancient viruses, fossils of decayed genes, such as TRIMCypA3, provide unique and specific insight into paleoviral infections that plagued primates deep in their evolutionary history.
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Fletcher AJ, Towers GJ. Inhibition of retroviral replication by members of the TRIM protein family. Curr Top Microbiol Immunol 2013; 371:29-66. [PMID: 23686231 DOI: 10.1007/978-3-642-37765-5_2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The TRIM protein family is emerging as a central component of mammalian antiviral innate immunity. Beginning with the identification of TRIM5α as a mammalian post-entry restriction factor against retroviruses, to the repeated observation that many TRIMs ubiquitinate and regulate signaling pathways, the past decade has witnessed an intense research effort to understand how TRIM proteins influence immunity. The list of viral families targeted directly or indirectly by TRIM proteins has grown to include adenoviruses, hepadnaviruses, picornaviruses, flaviviruses, orthomyxoviruses, paramyxoviruses, herpesviruses, rhabdoviruses and arenaviruses. We have come to appreciate how, through intense bouts of positive selection, some TRIM genes have been honed into species-specific restriction factors. Similarly, in the case of TRIMCyp, we are beginning to understand how viruses too have mutated to evade restriction, suggesting that TRIM and viruses have coevolved for millions of years of primate evolution. Recently, TRIM5α returned to the limelight when it was shown to trigger the expression of antiviral genes upon recognition of an incoming virus, a paradigm shift that demonstrated that restriction factors make excellent pathogen sensors. However, it remains unclear how many of ~100 human TRIM genes are antiviral, despite the expression of many of these genes being upregulated by interferon and upon viral infection. TRIM proteins do not conform to one type of antiviral mechanism, reflecting the diversity of viruses they target. Moreover, the cofactors of restriction remain largely enigmatic. The control of retroviral replication remains an important medical subject and provides a useful backdrop for reviewing how TRIM proteins act to repress viral replication.
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Affiliation(s)
- Adam J Fletcher
- MRC Centre for Medical Molecular Virology, University College, London, UK.
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41
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Betaretroviral envelope subunits are noncovalently associated and restricted to the mammalian class. J Virol 2012; 87:1937-46. [PMID: 23221553 DOI: 10.1128/jvi.01442-12] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The structure of the transmembrane subunit (TM) of the retroviral envelope glycoprotein (Env) is highly conserved among most retrovirus genera and includes a pair of cysteines that forms an intramolecular disulfide loop within the ectodomain. Alpha-, gamma-, and deltaretroviruses have a third cysteine, adjacent to the loop, which forms a disulfide bond between TM and the surface subunit (SU) of Env, while lentiviruses, which have noncovalently associated subunits, lack this third cysteine. The Betaretrovirus genus includes Jaagsiekte sheep retrovirus (JSRV) and mouse mammary tumor virus (MMTV), as well as many endogenous retroviruses. Envelope subunit association had not been characterized in the betaretroviruses, but lack of a third cysteine in the TM ectodomain suggested noncovalently associated subunits. We tested the Env proteins of JSRV and MMTV, as well as human endogenous retrovirus K (HERV-K)108--a betaretrovirus-like human endogenous retrovirus--for intersubunit bonding and found that, as in the lentiviruses, the Env subunits lack an intersubunit disulfide bond. Since these results suggest that the number of cysteines in the TM loop region readily distinguishes between covalent and noncovalent structure, we surveyed endogenous retroviral TM sequences in the genomes of vertebrates represented in public databases and found that (i) retroviruses with noncovalently associated subunits have been present during all of anthropoid evolution and (ii) the noncovalent env motif is limited to mammals, while the covalent type is found among five vertebrate classes. We discuss implications of these findings for retroviral evolution, cross-species transmissions, and recombination events involving the env gene.
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van der Kuyl AC, Berkhout B. The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus. Retrovirology 2012; 9:92. [PMID: 23131071 PMCID: PMC3511177 DOI: 10.1186/1742-4690-9-92] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 10/14/2012] [Indexed: 01/09/2023] Open
Abstract
Viruses often deviate from their hosts in the nucleotide composition of their genomes. The RNA genome of the lentivirus family of retroviruses, including human immunodeficiency virus (HIV), contains e.g. an above average percentage of adenine (A) nucleotides, while being extremely poor in cytosine (C). Such a deviant base composition has implications for the amino acids that are encoded by the open reading frames (ORFs), both in the requirement of specific tRNA species and in the preference for amino acids encoded by e.g. A-rich codons. Nucleotide composition does obviously affect the secondary and tertiary structure of the RNA genome and its biological functions, but it does also influence phylogenetic analysis of viral genome sequences, and possibly the activity of the integrated DNA provirus. Over time, the nucleotide composition of the HIV-1 genome is exceptionally conserved, varying by less than 1% per base position per isolate within either group M, N, or O during 1983–2009. This extreme stability of the nucleotide composition may possibly be achieved by negative selection, perhaps conserving semi-stable RNA secondary structure as reverse transcription would be significantly affected for a less A-rich genome where secondary structures are expected to be more stable and thus more difficult to unfold. This review will discuss all aspects of the lentiviral genome composition, both of the RNA and of its derived double-stranded DNA genome, with a focus on HIV-1, the nucleotide composition over time, the effects of artificially humanized codons as well as contributions of immune system pressure on HIV nucleotide bias.
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Affiliation(s)
- Antoinette C van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center of the University of Amsterdam, Meibergdreef 15, Amsterdam, AZ 1105, The Netherlands.
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Abstract
The emerging field of paleovirology aims to study the evolutionary age and impact of ancient viruses (paleoviruses) on host biology. Despite a historical emphasis on retroviruses, paleoviral 'fossils' have recently been uncovered from a broad swathe of viruses. These viral imprints have upended long-held notions of the age and mutation rate of viruses. While 'direct' paleovirology relies on the insertion of viral genes in animal genomes, examination of adaptive changes in host genes that occurred in response to paleoviral infections provides a complementary strategy for making 'indirect' paleovirological inferences. Finally, viruses have also impacted host biology by providing genes hosts have domesticated for their own purpose.
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Affiliation(s)
- Maulik R Patel
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle WA USA
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44
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Aswad A, Katzourakis A. Paleovirology and virally derived immunity. Trends Ecol Evol 2012; 27:627-36. [PMID: 22901901 DOI: 10.1016/j.tree.2012.07.007] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 07/11/2012] [Accepted: 07/16/2012] [Indexed: 01/04/2023]
Abstract
Paleovirology, the study of viruses on evolutionary timescales, can exploit information from endogenous viral elements (EVEs), which are the result of heritable horizontal gene transfer (HGT) from viruses to hosts. The availability of genomic data has increased opportunities to study EVEs, and bioinformatics techniques have been crucial in cataloguing EVE diversity and taxonomic coverage. Recent advances show that some EVEs have been co-opted as cellular genes, often as inhibitors of viral infection. These genes are an intriguing strategy in virus-host evolutionary battles in that genetic material is transferred from virus to host, and then used by the host against the virus. In this review, we consider the genes and processes involved in EVE-derived immunity (EDI), assess factors leading to its emergence, and outline how future work will benefit from incorporating evolutionary approaches.
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Affiliation(s)
- Amr Aswad
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
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45
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Abstract
In silico screening of metazoan genome data identified multiple endogenous hepadnaviral elements in the budgerigar (Melopsittacus undulatus) genome, most notably two elements comprising about 1.3 × and 1.0 × the full-length genome. Phylogenetic and molecular dating analyses show that endogenous budgerigar hepatitis B viruses (eBHBV) share an ancestor with extant avihepadnaviruses and infiltrated the budgerigar genome millions of years ago. Identification of full-length genomes with preserved key features like ε signals could enable resurrection of ancient BHBV.
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46
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Abstract
Recent years have seen a significant increase in understanding of the host genetic and genomic determinants of susceptibility to HIV-1 infection and disease progression, driven in large part by candidate gene studies, genome-wide association studies, genome-wide transcriptome analyses, and large-scale in vitro genome screens. These studies have identified common variants in some host loci that clearly influence disease progression, characterized the scale and dynamics of gene and protein expression changes in response to infection, and provided the first comprehensive catalogs of genes and pathways involved in viral replication. Experimental models of AIDS and studies in natural hosts of primate lentiviruses have complemented and in some cases extended these findings. As the relevant technology continues to progress, the expectation is that such studies will increase in depth (e.g., to include host whole exome and whole genome sequencing) and in breadth (in particular, by integrating multiple data types).
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Affiliation(s)
- Amalio Telenti
- Institute of Microbiology, University Hospital and University of Lausanne, 1011 Lausanne, Switzerland.
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47
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Feschotte C, Gilbert C. Endogenous viruses: insights into viral evolution and impact on host biology. Nat Rev Genet 2012; 13:283-96. [PMID: 22421730 DOI: 10.1038/nrg3199] [Citation(s) in RCA: 490] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recent studies have uncovered myriad viral sequences that are integrated or 'endogenized' in the genomes of various eukaryotes. Surprisingly, it appears that not just retroviruses but almost all types of viruses can become endogenous. We review how these genomic 'fossils' offer fresh insights into the origin, evolutionary dynamics and structural evolution of viruses, which are giving rise to the burgeoning field of palaeovirology. We also examine the multitude of ways through which endogenous viruses have influenced, for better or worse, the biology of their hosts. We argue that the conflict between hosts and viruses has led to the invention and diversification of molecular arsenals, which, in turn, promote the cellular co-option of endogenous viruses.
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Affiliation(s)
- Cédric Feschotte
- Department of Biology, University of Texas, Arlington, Texas 76016, USA.
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48
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Abstract
Endogenous retroviruses are a common component of the eukaryotic genome, and their evolution and potential function have attracted considerable interest. More surprising was the recent discovery that eukaryotic genomes contain sequences from RNA viruses that have no DNA stage in their life cycle. Similarly, several single-stranded DNA viruses have left integrated copies in their host genomes. This review explores some major evolutionary aspects arising from the discovery of these endogenous viral elements (EVEs). In particular, the reasons for the bias toward EVEs derived from negative-sense RNA viruses are considered, as well as what they tell us about the long-term "arms races" between hosts and viruses, characterized by episodes of selection and counter-selection. Most dramatically, the presence of orthologous EVEs in divergent hosts demonstrates that some viral families have ancestries dating back almost 100 million years, and hence are far older than expected from the phylogenetic analysis of their exogenous relatives.
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Affiliation(s)
- Edward C Holmes
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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49
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Fadel HJ, Saenz DT, Guevara R, von Messling V, Peretz M, Poeschla EM. Productive replication and evolution of HIV-1 in ferret cells. J Virol 2012; 86:2312-22. [PMID: 22171279 PMCID: PMC3302389 DOI: 10.1128/jvi.06035-11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 11/25/2011] [Indexed: 11/20/2022] Open
Abstract
A rodent or other small animal model for HIV-1 has not been forthcoming, with the principal obstacles being species-specific restriction mechanisms and deficits in HIV-1 dependency factors. Some Carnivorans may harbor comparatively fewer impediments. For example, in contrast to mice, the domestic cat genome encodes essential nonreceptor HIV-1 dependency factors. All Feliformia species and at least one Caniformia species also lack a major lentiviral restriction mechanism (TRIM5α/TRIMCyp proteins). Here we investigated cells from two species in another carnivore family, the Mustelidae, for permissiveness to the HIV-1 life cycle. Mustela putorius furo (domesticated ferret) primary cells and cell lines did not restrict HIV-1, feline immunodeficiency virus (FIV), equine infectious anemia virus (EIAV), or N-tropic murine leukemia virus (MLV) postentry and supported late HIV-1 life cycle steps comparably to human cells. The ferret TRIM5α gene exon 8, which encodes the B30.2 domain, was found to be pseudogenized. Strikingly, ferret (but not mink) cells engineered to express human HIV-1 entry receptors supported productive spreading replication, amplification, and serial passage of wild-type HIV-1. Nevertheless, produced virions had relatively reduced infectivity and the virus accrued G→A hypermutations, consistent with APOBEC3 protein pressure. Ferret cell-passaged HIV-1 also evolved amino acid changes in the capsid cyclophilin A binding loop. We conclude that the genome of this carnivore can provide essential nonreceptor HIV-1 dependency factors and that ferret APOBEC3 proteins with activity against HIV-1 are likely. Even so, unlike in cat cells, HIV-1 can replicate in ferret cells without vif substitution. The virus evolves in this novel nonprimate cell adaptive landscape. We suggest that further characterization of HIV-1 adaptation in ferret cells and delineation of Mustelidae restriction factor repertoires are warranted, with a view to the potential for an HIV-1 animal model.
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Affiliation(s)
- Hind J. Fadel
- Department of Molecular Medicine
- Division of Infectious Diseases, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Dyana T. Saenz
- Department of Molecular Medicine
- Department of Immunology
| | | | | | | | - Eric M. Poeschla
- Department of Molecular Medicine
- Department of Immunology
- Division of Infectious Diseases, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
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50
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Laguette N, Rahm N, Sobhian B, Chable-Bessia C, Münch J, Snoeck J, Sauter D, Switzer WM, Heneine W, Kirchhoff F, Delsuc F, Telenti A, Benkirane M. Evolutionary and functional analyses of the interaction between the myeloid restriction factor SAMHD1 and the lentiviral Vpx protein. Cell Host Microbe 2012; 11:205-17. [PMID: 22305291 DOI: 10.1016/j.chom.2012.01.007] [Citation(s) in RCA: 147] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 12/08/2011] [Accepted: 01/12/2012] [Indexed: 12/21/2022]
Abstract
SAMHD1 has recently been identified as an HIV-1 restriction factor operating in myeloid cells. As a countermeasure, the Vpx accessory protein from HIV-2 and certain lineages of SIV have evolved to antagonize SAMHD1 by inducing its ubiquitin-proteasome-dependent degradation. Here, we show that SAMHD1 experienced strong positive selection episodes during primate evolution that occurred in the Catarrhini ancestral branch prior to the separation between hominoids (gibbons and great apes) and Old World monkeys. The identification of SAMHD1 residues under positive selection led to mapping the Vpx-interaction domain of SAMHD1 to its C-terminal region. Importantly, we found that while SAMHD1 restriction activity toward HIV-1 is evolutionarily maintained, antagonism of SAMHD1 by Vpx is species-specific. The distinct evolutionary signature of SAMHD1 sheds light on the development of its antiviral specificity.
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Affiliation(s)
- Nadine Laguette
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Unité Propre de Recherche 1142, Laboratoires de Virologie Moléculaire, 34000 Montpellier, France
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